Unraveling the CLCC1 interactome: Impact of the Asp25Glu variant and its interaction with SigmaR1 at the Mitochondrial-Associated ER Membrane (MAM).

The endoplasmic reticulum (ER) plays an indispensable role in cellular processes, including maintenance of calcium homeostasis, and protein folding, synthesized and processing. Disruptions in these processes leading to ER stress and the accumulation of misfolded proteins can instigate the unfolded protein response (UPR), culminating in either restoration of balanced proteostasis or apoptosis. A key player in this intricate balance is CLCC1, an ER-resident chloride channel, whose essential role extends to retinal development, regulation of ER stress, and UPR.

Exploring basic science knowledge retention within a cohort of undergraduate medical students in the United Kingdom: A longitudinal study.

Background: Clinical reasoning is reliant on students having acquired a strong foundation in the basic sciences. However, there remains uncertainty regarding whether medical students are maintaining this knowledge over the span of their degrees. Therefore, this project aimed to assess long-term retention of basic science knowledge within a cohort of students from an undergraduate medical school in the United Kingdom (UK).

A blended future? A cross-sectional study demonstrating the impacts of the COVID-19 pandemic on student experiences of well-being, teaching and learning.

Introduction: The COVID-19 pandemic necessitated emergency changes to teaching, learning and assessment across higher education. Healthcare courses were particularly affected because of their interdependence with overstretched health services. We used this unprecedented situation to provide insight into how students react to unexpected crises and how institutions can most effectively support them.

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond.

There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. To streamline the process of integrating tools and constructing workflows as much as possible, we have developed Planemo, a software development kit for tool and workflow developers and Galaxy power users.

GalaxyCloudRunner: enhancing scalable computing for Galaxy.

Summary: The existence of more than 100 public Galaxy servers with service quotas is indicative of the need for an increased availability of compute resources for Galaxy to use. The GalaxyCloudRunner enables a Galaxy server to easily expand its available compute capacity by sending user jobs to cloud resources. User jobs are routed to the acquired resources based on a set of configurable rules and the resources can be dynamically acquired from any of four popular cloud providers (AWS, Azure, GCP or OpenStack) in an automated fashion.

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics.

The current state of much of the Wuhan pneumonia virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies and requires unimpeded access to data, analysis tools, and computational infrastructure. Here, we show that community efforts in developing open analytical software tools over the past 10 years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner.

The metabolic response to inflammation in astrocytes is regulated by nuclear factor-kappa B signaling.

Inflammation and metabolism are intrinsically linked with inflammatory stimuli inducing metabolic changes in cells and, in turn, metabolic capacity determining cellular inflammatory responses. Although well characterized in peripheral immune cells there is comparatively less known about these "immunometabolic" responses in astrocytes. In this study, we tested the hypothesis that the astrocytic inflammatory response driven by nuclear factor-kappa B (NF-κB) signaling is dependent on glycolytic metabolism.

A community effort to create standards for evaluating tumor subclonal reconstruction.

Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating them are lacking.

'The group was the only therapy which supported my needs, because it helped me feel normal and I was able to speak out with a voice': A qualitative study of an integrated group treatment for dual diagnosis service users within a community mental health setting.

Whilst the evidence for the efficacy of treatment interventions for individuals with dual diagnosis has been developing in recent decades, little is known about individual perceptions and the personal benefits of attending integrated treatment programmes within this population group. A qualitative methodology, Interpretive phenomenological analysis, was used to investigate the experiences of individuals with a range of complex mental health and coexisting substance misuse problems who took part in a psychoeducational group (PEG) programme. This comprised of social support and therapeutic peer group relationship facilitation.

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges.

Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the methods evaluated are reproducible and reusable is complicated by the diversity of software architectures, input and output file formats, and computing environments. To mitigate these problems, some challenges have leveraged new virtualization and compute methods, requiring participants to submit cloud-ready software packages.

STIM1 Is Required for Remodeling of the Endoplasmic Reticulum and Microtubule Cytoskeleton in Steering Growth Cones.

The spatial and temporal regulation of calcium signaling in neuronal growth cones is essential for axon guidance. In growth cones, the endoplasmic reticulum (ER) is a significant source of calcium signals. However, it is not clear whether the ER is remodeled during motile events to localize calcium signals in steering growth cones.

Copy number variation of in familial dystonic tremor.

Objective: To elucidate the genetic cause of a large 5 generation South Indian family with multiple individuals with predominantly an upper limb postural tremor and posturing in keeping with another form of tremor, namely, dystonic tremor.

Methods: Whole-genome single nucleotide polymorphism (SNP) microarray analysis was undertaken to look for copy number variants in the affected individuals.

Results: Whole-genome SNP microarray studies identified a tandem duplicated genomic segment of chromosome 15q24 present in all affected family members.

Basal fatty acid oxidation increases after recurrent low glucose in human primary astrocytes.

Aims/hypothesis: Hypoglycaemia is a major barrier to good glucose control in type 1 diabetes. Frequent hypoglycaemic episodes impair awareness of subsequent hypoglycaemic bouts. Neural changes underpinning awareness of hypoglycaemia are poorly defined and molecular mechanisms by which glial cells contribute to hypoglycaemia sensing and glucose counterregulation require further investigation.

Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa.

We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent.

Community-Driven Data Analysis Training for Biology.

The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials.

Practical Computational Reproducibility in the Life Sciences.

Many areas of research suffer from poor reproducibility, particularly in computationally intensive domains where results rely on a series of complex methodological decisions that are not well captured by traditional publication approaches. Various guidelines have emerged for achieving reproducibility, but implementation of these practices remains difficult due to the challenge of assembling software tools plus associated libraries, connecting tools together into pipelines, and specifying parameters. Here, we discuss a suite of cutting-edge technologies that make computational reproducibility not just possible, but practical in both time and effort.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging.

Truncating mutations underlie a spectrum of dominant hereditary motor neuropathies.

Objective: To identify the genetic cause of disease in 2 previously unreported families with forms of distal hereditary motor neuropathies (dHMNs).

Methods: The first family comprises individuals affected by dHMN type V, which lacks the cardinal clinical feature of vocal cord paralysis characteristic of dHMN-VII observed in the second family. Next-generation sequencing was performed on the proband of each family.

Choline transporter mutations in severe congenital myasthenic syndrome disrupt transporter localization.

The presynaptic, high-affinity choline transporter is a critical determinant of signalling by the neurotransmitter acetylcholine at both central and peripheral cholinergic synapses, including the neuromuscular junction. Here we describe an autosomal recessive presynaptic congenital myasthenic syndrome presenting with a broad clinical phenotype due to homozygous choline transporter missense mutations. The clinical phenotype ranges from the classical presentation of a congenital myasthenic syndrome in one patient (p.

A Novel Loss-of-Function Mutation in Associated with Autosomal Recessive Hereditary Congenital Facial Palsy in a Large Iranian Family.

Hereditary congenital facial palsy (HCFP) is a rare congenital cranial dysinnervation disorder, recognisable by non-progressive isolated facial nerve palsy (cranial nerve VII). It is caused by developmental abnormalities of the facial nerve nucleus and its nerve. So far, 4 homozygous mutations have been identified in 5 unrelated families (12 patients) with HCFP worldwide.

How does calcium interact with the cytoskeleton to regulate growth cone motility during axon pathfinding?

The precision with which neurons form connections is crucial for the normal development and function of the nervous system. The development of neuronal circuitry in the nervous system is accomplished by axon pathfinding: a process where growth cones guide axons through the embryonic environment to connect with their appropriate synaptic partners to form functional circuits. Despite intense efforts over many years to understand how this process is regulated, the complete repertoire of molecular mechanisms that govern the growth cone cytoskeleton and hence motility, remain unresolved.

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.

What does it take to convert a heap of sequencing data into a publishable result? First, common tools are employed to reduce primary data (sequencing reads) to a form suitable for further analyses (i.e., the list of variable sites).

Axons get ahead: Insights into axon guidance and congenital cranial dysinnervation disorders.

Cranial nerves innervate head muscles in a well-characterized and highly conserved pattern. Identification of genes responsible for human congenital disorders of these nerves, combined with the analysis of their role in axonal development in animal models, has advanced understanding of how neuromuscular connectivity is established. Here, we focus on the ocular motor system, as an instructive example of the success of this approach in unravelling the aetiology of human strabismus.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.

High-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses.